A fungus (plural: fungi[3] or funguses[4]) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants and animals.

A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Similar to animals, fungi are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesise. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (form a monophyletic group), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known as mycology (from the Greek μύκης mykes, mushroom). In the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants.

Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment. They have long been used as a direct source of human food, in the form of mushrooms and truffles; as a leavening agent for bread; and in the fermentation of various food products, such as wine, beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially and in detergents. Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals including humans. The fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g., rice blast disease) or food spoilage can have a large impact on human food supplies and local economies.

The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species, of which only 120,000 have been described. 8000 of them are detrimental to plants and 300 can be pathogenic to humans.[5] Ever since the pioneering 18th and 19th century taxonomical works of Carl Linnaeus, Christian Hendrik Persoon, and Elias Magnus Fries, fungi have been classified according to their morphology (e.g., characteristics such as spore color or microscopic features) or physiology. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, which has sometimes challenged the historical groupings based on morphology and other traits. Phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla.

Etymology

The English word fungus is directly adopted from the Latinfungus (mushroom), used in the writings of Horace and Pliny.[6] This in turn is derived from the Greek word sphongos (σφογγος "sponge"), which refers to the macroscopic structures and morphology of mushrooms and molds;[7] the root is also used in other languages, such as the German Schwamm ("sponge") and Schimmel ("mold").[8] The use of the word mycology, which is derived from the Greek mykes (μύκης "mushroom") and logos (λόγος "discourse"),[9] to denote the scientific study of fungi is thought to have originated in 1836 with English naturalist Miles Joseph Berkeley's publication The English Flora of Sir James Edward Smith, Vol. 5.[7] A group of all the fungi present in a particular area or geographic region is known as mycobiota (plural noun, no singular), e.g., "the mycobiota of Ireland".[10]

Characteristics

Before the introduction of molecular methods for phylogenetic analysis, taxonomists considered fungi to be members of the plant kingdom because of similarities in lifestyle: both fungi and plants are mainly immobile, and have similarities in general morphology and growth habitat. Like plants, fungi often grow in soil and, in the case of mushrooms, form conspicuous fruit bodies, which sometimes resemble plants such as mosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago.[11][12] Some morphological, biochemical, and genetic features are shared with other organisms, while others are unique to the fungi, clearly separating them from the other kingdoms:

With plants: Fungi have a cell wall[16] and vacuoles.[17] They reproduce by both sexual and asexual means, and like basal plant groups (such as ferns and mosses) produce spores. Similar to mosses and algae, fungi typically have haploid nuclei.[18]

The cells of most fungi grow as tubular, elongated, and thread-like (filamentous) structures called hyphae, which may contain multiple nuclei and extend by growing at their tips. Each tip contains a set of aggregated vesicles—cellular structures consisting of proteins, lipids, and other organic molecules—called the Spitzenkörper.[21] Both fungi and oomycetes grow as filamentous hyphal cells.[22] In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells.[14] There are also single-celled fungi (yeasts) that do not form hyphae, and some fungi have both hyphal and yeast forms.[23]

The fungal cell wall is composed of glucans and chitin; while glucans are also found in plants and chitin in the exoskeleton of arthropods,[25][26] fungi are the only organisms that combine these two structural molecules in their cell wall. Unlike those of plants and oomycetes, fungal cell walls do not contain cellulose.[27]

Most fungi lack an efficient system for the long-distance transport of water and nutrients, such as the xylem and phloem in many plants. To overcome this limitation, some fungi, such as Armillaria, form rhizomorphs,[28] which resemble and perform functions similar to the roots of plants. As eukaryotes, fungi possess a biosynthetic pathway for producing terpenes that uses mevalonic acid and pyrophosphate as chemical building blocks.[29] Plants and some other organisms have an additional terpene biosynthesis pathway in their chloroplasts, a structure fungi and animals do not have.[30] Fungi produce several secondary metabolites that are similar or identical in structure to those made by plants.[29] Many of the plant and fungal enzymes that make these compounds differ from each other in sequence and other characteristics, which indicates separate origins and convergent evolution of these enzymes in the fungi and plants.[29][31]

Diversity

Fungi have a worldwide distribution, and grow in a wide range of habitats, including extreme environments such as deserts or areas with high salt concentrations[32] or ionizing radiation,[33] as well as in deep sea sediments.[34] Some can survive the intense UV and cosmic radiation encountered during space travel.[35] Most grow in terrestrial environments, though several species live partly or solely in aquatic habitats, such as the chytrid fungus Batrachochytrium dendrobatidis, a parasite that has been responsible for a worldwide decline in amphibian populations. This organism spends part of its life cycle as a motile zoospore, enabling it to propel itself through water and enter its amphibian host.[36] Other examples of aquatic fungi include those living in hydrothermal areas of the ocean.[37]

Around 120,000 species of fungi have been described by taxonomists,[38] but the global biodiversity of the fungus kingdom is not fully understood.[38] A 2017 estimate suggests there may be between 2.2 and 3.8 million species.[39] In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based on morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy.[40] Species may also be distinguished by their biochemical and physiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction to chemical tests. The biological species concept discriminates species based on their ability to mate. The application of molecular tools, such as DNA sequencing and phylogenetic analysis, to study diversity has greatly enhanced the resolution and added robustness to estimates of genetic diversity within various taxonomic groups.[41]

Mycology

Mycology is the branch of biology concerned with the systematic study of fungi, including their genetic and biochemical properties, their taxonomy, and their use to humans as a source of medicine, food, and psychotropic substances consumed for religious purposes, as well as their dangers, such as poisoning or infection. The field of phytopathology, the study of plant diseases, is closely related because many plant pathogens are fungi.[42]

The use of fungi by humans dates back to prehistory; Ötzi the Iceman, a well-preserved mummy of a 5,300-year-old Neolithic man found frozen in the Austrian Alps, carried two species of polypore mushrooms that may have been used as tinder (Fomes fomentarius), or for medicinal purposes (Piptoporus betulinus).[43] Ancient peoples have used fungi as food sources–often unknowingly–for millennia, in the preparation of leavened bread and fermented juices. Some of the oldest written records contain references to the destruction of crops that were probably caused by pathogenic fungi.[44]

Morphology

Microscopic structures

Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10 µm in diameter and up to several centimeters in length. Hyphae grow at their tips (apices); new hyphae are typically formed by emergence of new tips along existing hyphae by a process called branching, or occasionally growing hyphal tips fork, giving rise to two parallel-growing hyphae.[48] Hyphae also sometimes fuse when they come into contact, a process called hyphal fusion (or anastamosis). These growth processes lead to the development of a mycelium, an interconnected network of hyphae.[23] Hyphae can be either septate or coenocytic. Septate hyphae are divided into compartments separated by cross walls (internal cell walls, called septa, that are formed at right angles to the cell wall giving the hypha its shape), with each compartment containing one or more nuclei; coenocytic hyphae are not compartmentalized.[49] Septa have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through; an example is the dolipore septum in fungi of the phylum Basidiomycota.[50] Coenocytic hyphae are in essence multinucleate supercells.[51]

Many species have developed specialized hyphal structures for nutrient uptake from living hosts; examples include haustoria in plant-parasitic species of most fungal phyla, and arbuscules of several mycorrhizal fungi, which penetrate into the host cells to consume nutrients.[52]

Although fungi are opisthokonts—a grouping of evolutionarily related organisms broadly characterized by a single posterior flagellum—all phyla except for the chytrids have lost their posterior flagella.[53] Fungi are unusual among the eukaryotes in having a cell wall that, in addition to glucans (e.g., β-1,3-glucan) and other typical components, also contains the biopolymer chitin.[54]

Macroscopic structures

Fungal mycelia can become visible to the naked eye, for example, on various surfaces and substrates, such as damp walls and spoiled food, where they are commonly called molds. Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies. These colonies can exhibit growth shapes and colors (due to spores or pigmentation) that can be used as diagnostic features in the identification of species or groups.[55] Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of a clonal colony of Armillaria solidipes, which extends over an area of more than 900 ha (3.5 square miles), with an estimated age of nearly 9,000 years.[56]

The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a cup-shaped fruit body that is often macroscopic and holds the hymenium, a layer of tissue containing the spore-bearing cells.[57] The fruit bodies of the basidiomycetes (basidiocarps) and some ascomycetes can sometimes grow very large, and many are well known as mushrooms.

Growth and physiology

Mold growth covering a decaying peach. The frames were taken approximately 12 hours apart over a period of six days.

The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellular turgor by producing osmolytes such as glycerol.[62] Adaptations such as these are complemented by hydrolytic enzymes secreted into the environment to digest large organic molecules—such as polysaccharides, proteins, and lipids—into smaller molecules that may then be absorbed as nutrients.[63][64][65] The vast majority of filamentous fungi grow in a polar fashion (extending in one direction) by elongation at the tip (apex) of the hypha.[66] Other forms of fungal growth include intercalary extension (longitudinal expansion of hyphal compartments that are below the apex) as in the case of some endophytic fungi,[67] or growth by volume expansion during the development of mushroom stipes and other large organs.[68] Growth of fungi as multicellular structures consisting of somatic and reproductive cells—a feature independently evolved in animals and plants[69]—has several functions, including the development of fruit bodies for dissemination of sexual spores (see above) and biofilms for substrate colonization and intercellular communication.[70]

Reproduction

Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this diverse kingdom of organisms.[74] It is estimated that a third of all fungi reproduce using more than one method of propagation; for example, reproduction may occur in two well-differentiated stages within the life cycle of a species, the teleomorph and the anamorph.[75] Environmental conditions trigger genetically determined developmental states that lead to the creation of specialized structures for sexual or asexual reproduction. These structures aid reproduction by efficiently dispersing spores or spore-containing propagules.

Asexual reproduction

Asexual reproduction occurs via vegetative spores (conidia) or through mycelial fragmentation. Mycelial fragmentation occurs when a fungal mycelium separates into pieces, and each component grows into a separate mycelium. Mycelial fragmentation and vegetative spores maintain clonal populations adapted to a specific niche, and allow more rapid dispersal than sexual reproduction.[76] The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) or Deuteromycota comprise all the species that lack an observable sexual cycle.[77]Deuteromycota is not an accepted taxonomic clade, and is now taken to mean simply fungi that lack a known sexual stage.

Sexual reproduction

Sexual reproduction with meiosis has been directly observed in all fungal phyla except Glomeromycota[78] (genetic analysis suggests meiosis in Glomeromycota as well). It differs in many aspects from sexual reproduction in animals or plants. Differences also exist between fungal groups and can be used to discriminate species by morphological differences in sexual structures and reproductive strategies.[79][80] Mating experiments between fungal isolates may identify species on the basis of biological species concepts.[80] The major fungal groupings have initially been delineated based on the morphology of their sexual structures and spores; for example, the spore-containing structures, asci and basidia, can be used in the identification of ascomycetes and basidiomycetes, respectively. Some species may allow mating only between individuals of opposite mating type, whereas others can mate and sexually reproduce with any other individual or itself. Species of the former mating system are called heterothallic, and of the latter homothallic.[81]

Most fungi have both a haploid and a diploid stage in their life cycles. In sexually reproducing fungi, compatible individuals may combine by fusing their hyphae together into an interconnected network; this process, anastomosis, is required for the initiation of the sexual cycle. Many ascomycetes and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited from the two parents do not combine immediately after cell fusion, but remain separate in the hyphal cells (see heterokaryosis).[82]

In ascomycetes, dikaryotic hyphae of the hymenium (the spore-bearing tissue layer) form a characteristic hook at the hyphal septum. During cell division, formation of the hook ensures proper distribution of the newly divided nuclei into the apical and basal hyphal compartments. An ascus (plural asci) is then formed, in which karyogamy (nuclear fusion) occurs. Asci are embedded in an ascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production of ascospores. After dispersal, the ascospores may germinate and form a new haploid mycelium.[83]

Sexual reproduction in basidiomycetes is similar to that of the ascomycetes. Compatible haploid hyphae fuse to produce a dikaryotic mycelium. However, the dikaryotic phase is more extensive in the basidiomycetes, often also present in the vegetatively growing mycelium. A specialized anatomical structure, called a clamp connection, is formed at each hyphal septum. As with the structurally similar hook in the ascomycetes, the clamp connection in the basidiomycetes is required for controlled transfer of nuclei during cell division, to maintain the dikaryotic stage with two genetically different nuclei in each hyphal compartment.[84] A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.[85] The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Morphology section).

In glomeromycetes (formerly zygomycetes), haploid hyphae of two individuals fuse, forming a gametangium, a specialized cell structure that becomes a fertile gamete-producing cell. The gametangium develops into a zygospore, a thick-walled spore formed by the union of gametes. When the zygospore germinates, it undergoes meiosis, generating new haploid hyphae, which may then form asexual sporangiospores. These sporangiospores allow the fungus to rapidly disperse and germinate into new genetically identical haploid fungal mycelia.[86]

Spore dispersal

Both asexual and sexual spores or sporangiospores are often actively dispersed by forcible ejection from their reproductive structures. This ejection ensures exit of the spores from the reproductive structures as well as traveling through the air over long distances.

Specialized mechanical and physiological mechanisms, as well as spore surface structures (such as hydrophobins), enable efficient spore ejection.[87] For example, the structure of the spore-bearing cells in some ascomycete species is such that the buildup of substances affecting cell volume and fluid balance enables the explosive discharge of spores into the air.[88] The forcible discharge of single spores termed ballistospores involves formation of a small drop of water (Buller's drop), which upon contact with the spore leads to its projectile release with an initial acceleration of more than 10,000 g;[89] the net result is that the spore is ejected 0.01–0.02 cm, sufficient distance for it to fall through the gills or pores into the air below.[90] Other fungi, like the puffballs, rely on alternative mechanisms for spore release, such as external mechanical forces. The bird's nest fungi use the force of falling water drops to liberate the spores from cup-shaped fruiting bodies.[91] Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.[92]

Other sexual processes

Besides regular sexual reproduction with meiosis, certain fungi, such as those in the genera Penicillium and Aspergillus, may exchange genetic material via parasexual processes, initiated by anastomosis between hyphae and plasmogamy of fungal cells.[93] The frequency and relative importance of parasexual events is unclear and may be lower than other sexual processes. It is known to play a role in intraspecific hybridization[94] and is likely required for hybridization between species, which has been associated with major events in fungal evolution.[95]

Evolution

In contrast to plants and animals, the early fossil record of the fungi is meager. Factors that likely contribute to the under-representation of fungal species among fossils include the nature of fungal fruiting bodies, which are soft, fleshy, and easily degradable tissues and the microscopic dimensions of most fungal structures, which therefore are not readily evident. Fungal fossils are difficult to distinguish from those of other microbes, and are most easily identified when they resemble extant fungi.[96] Often recovered from a permineralized plant or animal host, these samples are typically studied by making thin-section preparations that can be examined with light microscopy or transmission electron microscopy.[97] Researchers study compression fossils by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to examine surface details.[98]

The earliest fossils possessing features typical of fungi date to the Paleoproterozoic era, some 2,400 million years ago (Ma); these multicellular benthic organisms had filamentous structures capable of anastomosis.[99] Other studies (2009) estimate the arrival of fungal organisms at about 760–1060 Ma on the basis of comparisons of the rate of evolution in closely related groups.[100] For much of the Paleozoic Era (542–251 Ma), the fungi appear to have been aquatic and consisted of organisms similar to the extant chytrids in having flagellum-bearing spores.[101] The evolutionary adaptation from an aquatic to a terrestrial lifestyle necessitated a diversification of ecological strategies for obtaining nutrients, including parasitism, saprobism, and the development of mutualistic relationships such as mycorrhiza and lichenization.[102] Recent (2009) studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times.[103]

It is presumed that the fungi colonized the land during the Cambrian (542–488.3 Ma), long before land plants.[104] Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460 Ma) resemble modern-day Glomerales, and existed at a time when the land flora likely consisted of only non-vascular bryophyte-like plants.[105]Prototaxites, which was probably a fungus or lichen, would have been the tallest organism of the late Silurian. Fungal fossils do not become common and uncontroversial until the early Devonian (416–359.2 Ma), when they occur abundantly in the Rhynie chert, mostly as Zygomycota and Chytridiomycota.[104][106][107] At about this same time, approximately 400 Ma, the Ascomycota and Basidiomycota diverged,[108] and all modern classes of fungi were present by the Late Carboniferous (Pennsylvanian, 318.1–299 Ma).[109]

Lichen-like fossils have been found in the Doushantuo Formation in southern China dating back to 635–551 Ma.[110] Lichens formed a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 400 Ma;[111] this date corresponds to the age of the oldest known sporocarp fossil, a Paleopyrenomycites species found in the Rhynie Chert.[112] The oldest fossil with microscopic features resembling modern-day basidiomycetes is Palaeoancistrus, found permineralized with a fern from the Pennsylvanian.[113] Rare in the fossil record are the Homobasidiomycetes (a taxon roughly equivalent to the mushroom-producing species of the Agaricomycetes). Two amber-preserved specimens provide evidence that the earliest known mushroom-forming fungi (the extinct species Archaeomarasmius leggetti) appeared during the late Cretaceous, 90 Ma.[114][115]

Some time after the Permian–Triassic extinction event (251.4 Ma), a fungal spike (originally thought to be an extraordinary abundance of fungal spores in sediments) formed, suggesting that fungi were the dominant life form at this time, representing nearly 100% of the available fossil record for this period.[116] However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to assess,[117] the spike did not appear worldwide,[118][119] and in many places it did not fall on the Permian–Triassic boundary.[120]

Taxonomy

Although commonly included in botany curricula and textbooks, fungi are more closely related to animals than to plants and are placed with the animals in the monophyletic group of opisthokonts.[121] Analyses using molecular phylogenetics support a monophyletic origin of the Fungi.[41] The taxonomy of the Fungi is in a state of constant flux, especially due to recent research based on DNA comparisons. These current phylogenetic analyses often overturn classifications based on older and sometimes less discriminative methods based on morphological features and biological species concepts obtained from experimental matings.[122]

There is no unique generally accepted system at the higher taxonomic levels and there are frequent name changes at every level, from species upwards. Efforts among researchers are now underway to establish and encourage usage of a unified and more consistent nomenclature.[41][123] Fungal species can also have multiple scientific names depending on their life cycle and mode (sexual or asexual) of reproduction. Web sites such as Index Fungorum and ITIS list current names of fungal species (with cross-references to older synonyms).

The 2007 classification of Kingdom Fungi is the result of a large-scale collaborative research effort involving dozens of mycologists and other scientists working on fungal taxonomy.[41] It recognizes seven phyla, two of which—the Ascomycota and the Basidiomycota—are contained within a branch representing subkingdom Dikarya, the most species rich and familiar group, including all the mushrooms, most food-spoilage molds, most plant pathogenic fungi, and the beer, wine, and bread yeasts. The accompanying cladogram depicts the major fungal taxa and their relationship to opisthokont and unikont organisms, based on the work of Philippe Silar[124] and "The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research".[125] The lengths of the branches are not proportional to evolutionary distances.

Taxonomic groups

The major phyla (sometimes called divisions) of fungi have been classified mainly on the basis of characteristics of their sexual reproductive structures. Currently, seven phyla are proposed: Microsporidia, Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Glomeromycota, Ascomycota, and Basidiomycota.[41]

Phylogenetic analysis has demonstrated that the Microsporidia, unicellular parasites of animals and protists, are fairly recent and highly derived endobiotic fungi (living within the tissue of another species).[101][126] One 2006 study concludes that the Microsporidia are a sister group to the true fungi; that is, they are each other's closest evolutionary relative.[127] Hibbett and colleagues suggest that this analysis does not clash with their classification of the Fungi, and although the Microsporidia are elevated to phylum status, it is acknowledged that further analysis is required to clarify evolutionary relationships within this group.[41]

The Blastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota. Recent molecular data and ultrastructural characteristics, however, place the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and Basidiomycota). The blastocladiomycetes are saprotrophs, feeding on decomposing organic matter, and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids, most of which exhibit zygotic meiosis, the blastocladiomycetes undergo sporic meiosis.[101]

The Neocallimastigomycota were earlier placed in the phylum Chytridomycota. Members of this small phylum are anaerobic organisms, living in the digestive system of larger herbivorous mammals and in other terrestrial and aquatic environments enriched in cellulose (e.g., domestic waste landfill sites).[129] They lack mitochondria but contain hydrogenosomes of mitochondrial origin. As in the related chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.[41]

The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota.[40] These fungi form meiotic spores called ascospores, which are enclosed in a special sac-like structure called an ascus. This phylum includes morels, a few mushrooms and truffles, unicellular yeasts (e.g., of the genera Saccharomyces, Kluyveromyces, Pichia, and Candida), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and Claviceps. Many ascomycete species have only been observed undergoing asexual reproduction (called anamorphic species), but analysis of molecular data has often been able to identify their closest teleomorphs in the Ascomycota.[133] Because the products of meiosis are retained within the sac-like ascus, ascomycetes have been used for elucidating principles of genetics and heredity (e.g., Neurospora crassa).[134]

Unlike true fungi, the cell walls of oomycetes contain cellulose and lack chitin. Hyphochytrids have both chitin and cellulose. Slime molds lack a cell wall during the assimilative phase (except labyrinthulids, which have a wall of scales), and ingest nutrients by ingestion (phagocytosis, except labyrinthulids) rather than absorption (osmotrophy, as fungi, labyrinthulids, oomycetes and hyphochytrids). Neither water molds nor slime molds are closely related to the true fungi, and, therefore, taxonomists no longer group them in the kingdom Fungi. Nonetheless, studies of the oomycetes and myxomycetes are still often included in mycology textbooks and primary research literature.[138]

The Rozellida clade, including the "ex-chytrid" Rozella, is a genetically disparate group known mostly from environmental DNA sequences that is a sister group to fungi. Members of the group that have been isolated lack the chitinous cell wall that is characteristic of fungi.

The nucleariids, protists currently grouped in the Choanozoa (Opisthokonta), may be the next sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom.[121]

With plants

Mycorrhizal symbiosis between plants and fungi is one of the most well-known plant–fungus associations and is of significant importance for plant growth and persistence in many ecosystems; over 90% of all plant species engage in mycorrhizal relationships with fungi and are dependent upon this relationship for survival.[148]

The mycorrhizal symbiosis is ancient, dating to at least 400 million years ago.[130] It often increases the plant's uptake of inorganic compounds, such as nitrate and phosphate from soils having low concentrations of these key plant nutrients.[140][149] The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks".[150] A special case of mycorrhiza is myco-heterotrophy, whereby the plant parasitizes the fungus, obtaining all of its nutrients from its fungal symbiont.[151] Some fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes.[152] Similar to mycorrhiza, endophytic colonization by fungi may benefit both symbionts; for example, endophytes of grasses impart to their host increased resistance to herbivores and other environmental stresses and receive food and shelter from the plant in return.[153]

With algae and cyanobacteria

Lichens are a symbiotic relationship between fungi and photosyntheticalgae or cyanobacteria. The photosynthetic partner in the relationship is referred to in lichen terminology as a "photobiont". The fungal part of the relationship is composed mostly of various species of ascomycetes and a few basidiomycetes.[154] Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of biological succession,[155] and are prominent in some extreme environments, including polar, alpine, and semiarid desert regions.[156] They are able to grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and leaves.[157] As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis to the fungus, while the fungus provides minerals and water to the photobiont. The functions of both symbiotic organisms are so closely intertwined that they function almost as a single organism; in most cases the resulting organism differs greatly from the individual components. Lichenization is a common mode of nutrition for fungi; around 20% of fungi—between 17,500 and 20,000 described species—are lichenized.[158] Characteristics common to most lichens include obtaining organic carbon by photosynthesis, slow growth, small size, long life, long-lasting (seasonal) vegetative reproductive structures, mineral nutrition obtained largely from airborne sources, and greater tolerance of desiccation than most other photosynthetic organisms in the same habitat.[159]

As targets of mycoparasites

The organisms which parasitize fungi are known as mycoparasitic organisms. Certain species of the Pythium genus, which are oomycetes, have potential as biocontrol agents against certain fungi.[178] Fungi can also act as mycoparasites or antagonists of other fungi, such as Hypomyces chrysospermus, which grows on bolete mushrooms.

Mycotoxins are secondary metabolites (or natural products), and research has established the existence of biochemical pathways solely for the purpose of producing mycotoxins and other natural products in fungi.[29] Mycotoxins may provide fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivory).[181][182] Many fungal secondary metabolites (or derivatives) are used medically, as described under Human Use below.

Pathogenic mechanisms

Ustilago maydis is a pathogenic plant fungus that causes smut disease in maize and teosinte. Plants have evolved efficient defense systems against pathogenic microbes such as U. maydis. A rapid defense reaction after pathogen attack is the oxidative burst where the plant produces reactive oxygen species at the site of the attempted invasion. U. maydis can respond to the oxidative burst with an oxidative stress response, regulated by the gene YAP1. The response protects U. maydis from the host defense, and is necessary for the pathogen’s virulence.[183] Furthermore, U. maydis has a well-established recombinational DNA repair system which acts during mitosis and meiosis.[184] The system may assist the pathogen in surviving DNA damage arising from the host plant’s oxidative defensive response to infection.[185]

Cryptococcus neoformans is an encapsulated yeast that can live in both plants and animals. C. neoformans usually infects the lungs, where it is phagocytosed by alveolar macrophages.[186] Some C. neoformans can survive inside macrophages, which appears to be the basis for latency, disseminated disease, and resistance to antifungal agents. One mechanism by which C. neoformans survives the hostile macrophage environment is by up-regulating the expression of genes involved in the oxidative stress response.[186] Another mechanism involves meiosis. The majority of C. neoformans are mating "type a". Filaments of mating "type a" ordinarily have haploid nuclei, but they can become diploid (perhaps by endoduplication or by stimulated nuclear fusion) to form blastospores. The diploid nuclei of blastospores can undergo meiosis, including recombination, to form haploid basidiospores that can be dispersed.[187] This process is referred to as monokaryotic fruiting. this process requires a gene called DMC1, which is a conserved homologue of genes recA in bacteria and RAD51 in eukaryotes, that mediates homologous chromosome pairing during meiosis and repair of DNA double-strand breaks. Thus, C. neoformans can undergo a meiosis, monokaryotic fruiting, that promotes recombinational repair in the oxidative, DNA damaging environment of the host macrophage, and the repair capability may contribute to its virulence.[185][187]

Certain types of cheeses require inoculation of milk curds with fungal species that impart a unique flavor and texture to the cheese. Examples include the blue color in cheeses such as Stilton or Roquefort, which are made by inoculation with Penicillium roqueforti.[214] Molds used in cheese production are non-toxic and are thus safe for human consumption; however, mycotoxins (e.g., aflatoxins, roquefortine C, patulin, or others) may accumulate because of growth of other fungi during cheese ripening or storage.[215]

Poisonous fungi

Many mushroom species are poisonous to humans, with toxicities ranging from slight digestive problems or allergic reactions as well as hallucinations to severe organ failures and death. Genera with mushrooms containing deadly toxins include Conocybe, Galerina, Lepiota, and, the most infamous, Amanita.[216] The latter genus includes the destroying angel (A. virosa) and the death cap (A. phalloides), the most common cause of deadly mushroom poisoning.[217] The false morel (Gyromitra esculenta) is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw.[218]Tricholoma equestre was considered edible until it was implicated in serious poisonings causing rhabdomyolysis.[219]Fly agaric mushrooms (Amanita muscaria) also cause occasional non-fatal poisonings, mostly as a result of ingestion for its hallucinogenic properties. Historically, fly agaric was used by different peoples in Europe and Asia and its present usage for religious or shamanic purposes is reported from some ethnic groups such as the Koryak people of north-eastern Siberia.[220]

As it is difficult to accurately identify a safe mushroom without proper training and knowledge, it is often advised to assume that a wild mushroom is poisonous and not to consume it.[221][222]